I am unsure what will occur with your replication jobs when deploy the changes to the target database. From the limited experience with database replication, I suspect that something will go wrong.

SQL Data Compare will not drop the primary key constraint if it is the Comparison key used for the comparison of the data, even if you have the option to Drop primary keys, Indexes and unique constraints enabled.

I recommend if you have a test environment with replication configured, that you perform some tests to see what will occur with your replication jobs.

Also backup the target database before running the deployment wizard against the target database, so you can recover the database if something does go wrong with the deployment causing a loss of data.